Variant report

Variant	rs1138120
Chromosome Location	chr22:30229954-30229955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr22:30229783-30230611	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30228718..30231367-chr22:30232651..30236541,5	K562	blood:
2	chr22:30228546..30230856-chr22:30232707..30235317,4	MCF-7	breast:
3	chr22:30226725..30230027-chr22:30233173..30235923,3	MCF-7	breast:
4	chr22:30225765..30230715-chr22:30232604..30236000,6	K562	blood:

Variant related genes	Relation type
ASCC2	TF binding region
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs131293	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs131295	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131301	0.94[ASN][1000 genomes]
rs140145	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs140149	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140150	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17711377	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057882	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074706	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2074707	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2079338	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2301402	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs249398	0.97[ASN][1000 genomes]
rs28749829	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36574	0.93[ASN][1000 genomes]
rs36576	0.97[ASN][1000 genomes]
rs5752961	0.96[ASN][1000 genomes]
rs5752964	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763512	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997529	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997530	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997535	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6006274	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs713656	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713657	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740041	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs81800	0.96[ASN][1000 genomes]
rs9306465	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9614055	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1138120	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
3	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
4	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
9	chr22:30208800-30231200	Strong transcription	Lung	lung
10	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:30215000-30230800	Strong transcription	Fetal Brain Female	brain
13	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:30218000-30230600	Strong transcription	Fetal Thymus	thymus
15	chr22:30218000-30231000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr22:30218200-30232200	Strong transcription	Fetal Intestine Small	intestine
17	chr22:30218400-30233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr22:30218600-30230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:30218600-30233400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:30219000-30232000	Weak transcription	Fetal Brain Male	brain
21	chr22:30219600-30233400	Weak transcription	Fetal Kidney	kidney
22	chr22:30220000-30231600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr22:30221400-30233400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr22:30221600-30233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:30221800-30233400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr22:30221800-30233600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr22:30222000-30232800	Weak transcription	Hela-S3	cervix
28	chr22:30222000-30233600	Weak transcription	Small Intestine	intestine
29	chr22:30223000-30230400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr22:30223000-30230600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr22:30223000-30230600	Strong transcription	Thymus	Thymus
32	chr22:30223000-30230600	Strong transcription	Dnd41	blood
33	chr22:30223000-30230600	Strong transcription	HSMM	muscle
34	chr22:30223000-30231000	Strong transcription	Primary B cells from cord blood	blood
35	chr22:30223000-30231200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr22:30223000-30231600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:30223000-30232200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr22:30223000-30232200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr22:30223000-30232200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr22:30223200-30230600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr22:30223200-30230600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr22:30223400-30231600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr22:30223600-30230600	Strong transcription	Spleen	Spleen
44	chr22:30223800-30231200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr22:30224000-30230800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr22:30224200-30233200	Weak transcription	Right Atrium	heart
47	chr22:30224400-30230000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr22:30224400-30230800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:30224400-30230800	Strong transcription	Brain Hippocampus Middle	brain
50	chr22:30224400-30231000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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